[Bioc-devel] possible bug in Rhtslib::pkgconfig

[Aaron Lun]

The "Re:" in the title of this e-mail? I add an "Re:" to all my titles,
and I assume that the mailing list dispatcher adds the "[Bioc-devel]"
tag (cleverly inserting it between the "Re:" and the actual title).

Just looked it up - apparently it stands for "in re" in Latin. I guess I
learn something new every day.

Martin Morgan wrote:
> Thanks Aaron I'll follow up on the support site.
>
> Can you clarify where the 'Re:' came from in the title? I can't find a
> previous post with similar title.
>
> Martin
>
> On 10/27/2017 05:42 AM, Aaron Lun wrote:
>> Dear list,
>>
>> It seems that there is an issue with Rhtslib::pkgconfig() regarding the
>> identification of the location of the shared library on some systems:
>>
>> https://support.bioconductor.org/p/102248/
>>
>> To summarize: on this system, R is putting the shared library in lib64/,
>> while pkgconfig() looks for it in lib/. This results in linkage errors
>> for all packages depending on Rhtslib on this system. I imagine that the
>> same would happen for all library packages, e.g., beachmat, Rhdf5lib.
>>
>> Looking at the Makevars for Rhtslib suggests that the shared library is
>> stored in ${R_PACKAGE_DIR}/lib${R_ARCH}, while pkgconfig only ever looks
>> in lib/. I assume that this usually works because ${R_ARCH} is empty on
>> most linux systems, though perhaps this cannot be guaranteed.
>>
>> Cheers,
>>
>> Aaron
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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